Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF BENZOYLFORMATE DECARBOXYLASE MUTANT L403S
 
Authors :  W. R. P. Novak, F. H. Andrews, A. R. Tom, P. R. Gunderman, M. J. Mcleish
Date :  15 Aug 12  (Deposition) - 22 May 13  (Release) - 22 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.26
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Decarboxylase, Thiamin Thiazolone Diphosphate Cofactor, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. H. Andrews, A. R. Tom, P. R. Gunderman, W. R. Novak, M. J. Mcleish
A Bulky Hydrophobic Residue Is Not Required To Maintain The V-Conformation Of Enzyme-Bound Thiamin Diphosphate.
Biochemistry V. 52 3028 2013
PubMed-ID: 23607689  |  Reference-DOI: 10.1021/BI400368J

(-) Compounds

Molecule 1 - BENZOYLFORMATE DECARBOXYLASE
    ChainsA
    EC Number4.1.1.7
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET24
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneMDLC
    MutationYES
    Organism ScientificPSEUDOMONAS PUTIDA
    Organism Taxid303
    SynonymBFD, BFDC

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (4x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2GOL2Ligand/IonGLYCEROL
3NA1Ligand/IonSODIUM ION
4TZD1Ligand/Ion2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGENDIPHOSPHATE
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL8Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
4TZD4Ligand/Ion2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGENDIPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:428 , ASN A:455 , THR A:457 , TZD A:606 , HOH A:724BINDING SITE FOR RESIDUE CA A 601
2AC2SOFTWAREGLU A:37 , ASP A:364 , HOH A:775 , HOH A:898 , HOH A:1051 , HOH A:1072 , HOH A:1103 , HOH A:1118 , HOH A:1168BINDING SITE FOR RESIDUE CA A 602
3AC3SOFTWAREASN A:117 , LEU A:118 , ARG A:120BINDING SITE FOR RESIDUE NA A 603
4AC4SOFTWAREALA A:196 , ARG A:294 , ILE A:296 , ASP A:312 , HOH A:785 , HOH A:1126BINDING SITE FOR RESIDUE GOL A 604
5AC5SOFTWARELEU A:43 , GLN A:443 , GLY A:475 , LEU A:476 , ASP A:477 , HOH A:1031 , HOH A:1128 , HOH A:1217BINDING SITE FOR RESIDUE GOL A 605
6AC6SOFTWAREASN A:23 , PRO A:24 , GLY A:25 , GLU A:47 , HIS A:70 , ASN A:77 , GLU A:375 , THR A:377 , SER A:378 , GLY A:401 , GLY A:402 , SER A:403 , GLY A:427 , ASP A:428 , GLY A:429 , SER A:430 , TYR A:433 , ASN A:455 , THR A:457 , TYR A:458 , GLY A:459 , ALA A:460 , CA A:601 , HOH A:730 , HOH A:1226BINDING SITE FOR RESIDUE TZD A 606

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GM1)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Arg A:120 -Pro A:121
2Ala A:149 -Pro A:150
3Val A:277 -Phe A:278

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GM1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GM1)

(-) Exons   (0, 0)

(no "Exon" information available for 4GM1)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:525
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4gm1a1 A:2-181 automated matches                                                                                                                                                   d4gm1a2 A:182-341 Benzoylformate decarboxylase                                                                                                                  d4gm1a3 A:342-526 automated matches                                                                                                                                                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...eeee..hhhhhhhhh......eeee..hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhh........hhhhh.......ee...hhhhhhhhhhhhhhhhhh.....eeeeee.hhh....hhhhhhhh..........hhhhhhhhhhhhhhh...eeeehhhhhhh.hhhhhhhhhhhhh..eee...............eeee...hhhhhhhhhh...eeeee....................eeeeee.hhhhhhhh...eeee.hhhhhhhhhhhhh........................hhhhhhhhhhhhh....eeeee...hhhhhhhhh.......eee.......hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhh.............hhhhhhhhhh.eeeee.hhhhhhhhhhhhhh....eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gm1 A   2 ASVHGTTYELLRRQGIDTVFGNPGSNELPFLKDFPEDFRYILALQEACVVGIADGYAQASRKPAFINLHSAAGTGNAMGALSNAWNSHSPLIVTAGQQTRAMIGVEALLTNVDAANLPRPLVKWSYEPASAAEVPHAMSRAIHMASMAPQGPVYLSVPYDDWDKDADPQSHHLFDRHVSSSVRLNDQDLDILVKALNSASNPAIVLGPDVDAANANADCVMLAERLKAPVWVAPSAPRCPFPTRHPCFRGLMPAGIAAISQLLEGHDVVLVIGAPVFRYHQYDPGQYLKPGTRLISVTCDPLEAARAPMGDAIVADIGAMASALANLVEESSRQLPTAAPEPAKVDQDAGRLHPETVFDTLNDMAPENAIYLNESTSTTAQMWQRLNMRNPGSYYFCAAGGSGFALPAAIGVQLAEPERQVIAVIGDGSANYSISALWTAAQYNIPTIFVIMNNGTYGALRWFAGVLEAENVPGLDVPGIDFRALAKGYGVQALKADNLEQLKGSLQEALSAKGPVLIEVSTVSP 526
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521     

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 3)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GM1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GM1)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TZD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:149 - Pro A:150   [ RasMol ]  
    Arg A:120 - Pro A:121   [ RasMol ]  
    Val A:277 - Phe A:278   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4gm1
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  MDLC_PSEPU | P20906
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  4.1.1.7
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  MDLC_PSEPU | P20906
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MDLC_PSEPU | P209061bfd 1mcz 1pi3 1po7 1q6z 1yno 2fn3 2fwn 2v3w 3f6b 3f6e 3fsj 3fzn 4gg1 4gm0 4gm4 4gp9 4gpe 4jd5 4ju8 4ju9 4jua 4jub 4juc 4jud 4juf 4k9k 4k9l 4k9m 4k9n 4k9o 4k9p 4mpj 4mpp 4mpr 4mq5 4mzx 4qel 5dei 5dgd 5dgt

(-) Related Entries Specified in the PDB File

4gg1 4gm0 4gm4